Dont Mess with Big Brother
by dragonslayer111
Summary: Leo was away on his training trip in Japan but when he returns he finds his sensei badly hurt his home destroyed and his brothers under the control of the New Shredder, what will Leo do to get his Little brothers back!
1. Chapter 1

**This is my first Ninja turtle's fanfiction. I have been in a turtle mood for a little while and I can't get this story out of my head, I thought if I write it I can finally get it out of my head and finish my other stories.**

 **I didn't want to start another story because I have a lot of other stories going on right now and I told myself that I would not start another story until I finished one of my fairy tail stories. (well that didn't happen).**

 **I promise I did not abandon any of my other stories if you are people that have read them. I will continue those stories.**

 **Ok so for this story I took some things from both the 2003 universe and the 2012 universe like Hun from the 2003 because I don't like the Hun from the 2012 turtles. Also, I am using some mutants from the 2012 universe because I like some of them and I couldn't decide which turtle verse to use. So, you can really pick which one you like best I will not describe things all that much because the two turtle verses have a lot of differences and I don't want to confuse anyone. I hope you enjoy!**

"Pack your things Leonardo you will be leaving for japan tomorrow." The three turtles gasped from outside the closed door the master Splinter's room. Yes, it was Ture that Leo hasn't been acting like himself in truth he was acting more like Raph; his clam demeaner disappeared and repapered in a blink of an eye he snapped at everyone more and he just wasn't himself.

Mikey said it was because he was under a lot of stress by his repeated failures, his quilt and picking up his younger brothers slake. A little stress was understandable… wasn't it I mean it must be hard to be the leader and the oldest of four teenage mutant turtles, but this just wasn't Leo. Even with the way Leo was acting it didn't justify sending him away… right.

Leo bowed to master Splinter as he resigned to his fate. He stood to pack his things his younger brothers running away from the door and pretending that they were not ease dropping on the two. Leo closed the door behind him and sighed he looked up for a brief second and looked at his three younger brothers, with another sigh he disappeared into his room.

Leonardo left late that night to catch the last cargo ship that was leaving for japan he moved swiftly though the shadows careful not to be seen; as the ship pulled out of the dock he said goodbye to New York, to his life there he said goodbye to his friends and his brothers that he didn't say good bye too personally because he felt that if he saw them cry and telling him to stay he would not be able to leave he might as well break down too and that was the last thing his brothers needed to see from their fearless leader. He was already not acting like himself and he knew it he was always angry and mad at himself for getting his family hurt, the family he would gladly die protecting; and now he was going across the world where he could not see his beloved family much less protect them when they needed it.

Who was going to make sure Raph didn't lose control or have someone to beat on when he was upset. Who was going to make sure Donny ate or went to sleep after getting engrossed in his work and who was going to protect Mikey from his nightmares someone to tell him everything would be alright because big brother was there.

Of course, the way he was acting he wasn't sure if anything was alright or ever was. His brothers had distance themselves from Leo ever since their last encounter with the Shredder he was acting more like a monster then the calm, in control older brother he was supposed to be. Leo quietly let out a chuckle; it was now that he realized what he was doing when he was on a ship destined to Japan. His brothers would be fine without him, and with that thought in mind he drifted off to sleep.

 **Back in the lair Next morning**

"he left without saying a signal word of goodbye!" Raph shouted

"relax Raph I am sure Leo had his reasons." Donatello said trying and failing to calm his hot headed older brother.

"that jerk has been all moody and then he just leaves what are we to him?!" he continued to shout the three-remaining brothers had worked up a lot later then they normally do Leo was the one to walk them up for morning training and with resent events they needed the sleep. They all hope Leo would have waited so they can all say their goodbyes before he left, but when they woke up they found he was already gone.

"Raph calm down please." Mikey said tears coming into his eyes. Being the youngest of four was hard and he did try his best to be like them that meant no crying over stupid things he acted stupid and goofy because sometimes that was the only way he didn't feel like he was suffocating in Raph's anger when Don locks himself in the lab or Leo's seriousness he felt if he did nothing else for the family his jokes and care free attitude could brighten his brothers moods as well; but then there were times like this where he felt has hopeless and without Leo to defuse the situation he didn't know what to do.

"Raphael!" Master Splinter shouted the air in the room seamed to freeze as his voice echoed off the walls. "that is enough you need to except that Leonardo is gone and you need to start and take responsibility in your brother's absence, do I make myself clear."

"but Master- "

"do I make myself clear." He said in a more demanding tone that made the three flinch

"yes, Master Splinter" Raph said as he turned and bumped into Don on his way to his room and away from the embarrassment he was feeling.

'this will take some getting used to.' Splinter thought as turned and disappeared back into his room to meditated some more. This left Mikey and Don in the main room staring at the doors their family had gone through taking in the silence in their home.

'Leo come back soon we miss you.' Mikey thought as he too left.

 **Well I hope you liked the first chapter of my first Ninja turtle story.**


	2. Chapter 2

**I hope you like the first chapter and here is the second**

"Michelangelo how long have you been working on that?" Splinter asked as he watched his youngest son build a town out of playing cards.

"umm I'm not sure Raph what time is it?" Micky asked as he placed another two cards on his tower

"does it look like I wear a watch ask Don." Raph said as he sent other two punches to the dummy

"Don what time is it?" Mikey asked again

"I don't know ask Leo!" he said only for everyone to freeze and stare at one another before looking at their master

"Master Splinter when is Leo coming back?" Raph asked walking over to their make-shift living room

"he has been gone over a two months now." Donny said looking down during the two months they kept forget Leo was gone and would call out to him or look to him for something and then realize he isn't there this was mostly difficult the first few weeks after he left. Now every time someone mentions Leo the room goes quite almost like they are guilty for bring it up, they all try to forget Leo isn't there.

"I am not sure my sons he has a lot to work though in his mind and his heart." Their father looked down he too was missing Leonardo.

"uhggg I just wish things would go back to normal we have been stuck down here the entire time Leo's been gone I am starting to go stir crazy!" Raph shouted

"Raphael, it is dangerous on the surface you mustn't go out there until your brother returns."

"right because everything is better when the mighty Leonardo is there to protect us!" He huffed and stormed to his room making a point to nock Mikey's towner over, and to reserve a loud Hey from the orange clad turtle.

"I wonder why you didn't send him to Japan." Donnie mumbled as he turned back to his work. Master Splinter sighed at his second eldest quick anger.

As quickly as their peace returned an alarm started to sound Don quickly got up and ran to the monitors with the rest of his family close behind him.

"What is it Donatello?" the old rat asked with concerned eyes

"Well it looks like April send a distress signal from her place." He said franticly typing on the computer

"Well what are we waiting for let's go save her!" Raph shouted as he twirled his Sai

"My sons it is too dangerous"

"No offence Master Splinter but we can't wait for Leo to return to rescue a friend." Raph said as the three turtles ran out of the Lair.

 **At Aprils a little earlier**

'today has been a slow day.' April thought to herself as her head rested in her hand, she looked over her empty shop.

"I wonder how the boys are doing?" she said aloud to no one in particular she hasn't seen the boys for over two months she had called but Donnie said they were keeping a low profile for a while not really telling her why, of course she did not complain the turtles have been running around almost non-stop taking out the purple dragons and the foot ninja they deserved a break.

She thought about going down as well just to say hi but she thought against it she found she needed a break to from all the craziness that comes with knowing the teenage mutant ninja turtles. She also thought this would be a good time to work on her store and actually have it open for business but there are always days like today where she would be lucky to even get one person in the shop, it was also days like this that she missed the turtles the most.

April's eyes snapped open when she heard the ding of her door opening "hello welcome to my shop if you need anything I would-" she cut herself off when she recognized the person at the door. "Casey what are you doing here?"

"I came to see you." He said both blushing slightly "it doesn't look like you have to many customers … would you like to go down to visit the guys it's been awhile."

"I would love to Casey but I really need to keep the shop open for a full day before I go running off." She sighed almost regretting what she just said. Just then the door opened again but instead of the customer she was hoping to see five-foot ninja came into the shop.

"Not again!" April cried as Casey began fighting the ninja but Casey was having trouble fighting these ninjas has they were better trained then he remembered them being. So, both Casey and April were over run and now they were held by them. The door opened again and a dark hooded figure walked in and chuckled at the sight before them.

"Who are you!" Casey shouted as he struggled against the ninja holding him.

"Who am I? I am the person that will destroy the turtles!" the figure said as they lifted the hood to show a very familiar smiling face

"Karai!" they shouted

"What do you want!" April said shooting her best glare at the ninja, despite the fear she felt inside.

"I want the turtles, now tell me where they are!" she demanded

"We won't tell you anything!" Casey shouted

"I want the location of their lair." Karai said again her voice begin to sound annoyed along with her usual cruel tone.

"You just wait Karai they will be here soon and they will make short work of you and your ninja!" April shouted before she even knew what she was saying. It didn't seam she spoke to soon because just then three human sized turtles knocked out the ninja's holding their friends.

"You wanted us well here we are!" Raph shouted

"Only three of you where is Leonardo?" Karai asked not at all surprised that her five ninjas were taken out

"Wouldn't you like to know." Mikey said as more ninja began to poor in at all sizes.

"No not my shop not again!" April cried the turtles carried the fight to the roof tops and away from Aprils shop so they didn't destroy it again but now they were thinking that was a mistake because they were being surrounded

"Raph what the plan!" Mikey shouted as he punched on ninja in the gut and hit two on the head with his chucks.

"Raph there are too many we are being surrounded!" Donnie shouted as he knocked several ways with his bow staff.

Raph couldn't think; he wasn't used to leading his brother he wasn't used to being asked for what to do next normally he would worry about what he was doing in a fight and then Leo would come up with a plan, he would give him a hard time about it and they would win and go home. But Leo wasn't here and now the responsibility landed on him and he didn't know what to do. Maybe Splinter was right it was too dangerous when their was only three of them.

"Raph!" both his little brothers yelled to grab his attention he looked over at them he saw Donnie was boxed in and Mikey was trying to get to his brother but got hit on the head. Raph then was hit and sent flying from Karai kicking him in the back.

"Micky, Don!" Raph shouted now he was mad. For him everything when red and he shot to his feet punching and kicking the foot ninja left and right trying to get to his brothers. Before he knew it all the ninja just disappeared. Not thinking much into it he ran as fast as he could to his closes brother which happened to be Donatello; who was slowly getting back to his feet and using his jo as a cane.

"Mikey are you ok?" Raph called behind him as he helped Donnie the rest of the way to his feet. When he didn't get an answer, he turned looking in the direction he last saw Mikey but nothing was there. "this isn't funny Mikey come out!" Raph shouted annoyed at their youngest brother. Again, there was no answer

"Mikey!?" Donnie called but he too did not get a response back. Raph left Don to scowler the roof tops looking for their now missing brother after ten minutes and not finding anything he went back to Donnie's side.

"Anything?" Don asked. Raph shook his head not trusting his voice to speak "what? You don't think…" he didn't need to finish that sentence they knew the dark truth the foot had their little brother and at that moment they couldn't do anything.

Normally Raph would go running off looking for his baby brother he would march into foot head corners and demanded his brother back he was still planning on doing just that but right now he had to get Donnie home.

 **Raph's POV**

Back in the Lair I was sitting on the couch waiting for Master Splinter to come out of the infirmary after he fixed up Don. My mind began to wondered what would Leo do if he was in this situation he would probably forcing me to calm down and come back home so they could come up with a plan to get Mikey back I would yell at him that they should just run in there and take out who ever got in their way, then Leo would tell me everything wrong with that plan then find a way to calm me down like he always does… or at least what he used to do before that final showdown with the Shredder.

Now I am not sure, now I am the oldest and I am so lost on what to do. I let out a low growl and stood up; I walked over to my favorite punching bag. This always helped me to let out some steam and to think.

Punch, punch, punch my mind went back to the fight on the roof top; punch Donnie and Mikey calling my name, punch everything going red, punch then everything just disappeared Mikey disappeared I gave a really hard punch making the bag to go flying off the chain.

"Raphael." I turned to see Splinter standing behind me.

"I am so sorry I failed Mikey… it's my fault he's gone, if I was thinking differently if Leo was here-" I said tears threated to fall my shoulders slumped as I turned away from my sensei

"Raphael none of this is your fault you wanted to go to miss O'Neil's add."

"But I got Don hurt and Mikey's gone!" I shouted my anger returning

"Yes, and we will get him back but I am proud of you that you did not run off looking for him or going after the foot when you had another brother in need." Master Splinter said

Why was he not yelling at me why was he not disappointed in me? I didn't understand I messed up and he said he was proud of me for trying and bringing Donnie home if Leo did half of what I did he would have gotten a lecture why?

I did not voice my opinions and before Splinter could say anything else the door opened to revile April and Casey.

 **Normal POV**

"Guys I am so glad you are ok you guys didn't come back to the shop after you lead the ninjas away." April said

"Where was Leo I didn't see him there?" Casey asked with a serious tone after he saw how Raph was acting April picked up on this mood to she knew something was wrong.

"And where is Don and Mikey." April asked

"Leo left." Don said as he stepped out of the infirmary his ankle was wrapped and he was still using his bow staff as a cane.

"Don! What do you mean Leo left where is he?" April yelled as she ran up to the injured turtle

"He is on a journey to find himself." Master Splinter said somewhat regretting that he banished his eldest son to Japan.

"And Mikey well the foot has him." Raph said quietly

The two humans looked at each other with worried expressions.

"Don't worry we will get Mikey back." They said with determination.

 **So, I hope you liked this chapter Mikey is gone and the war is just beginning**.


	3. Chapter 3

**Chapter 3: I fixed some of my mistakes in the first two chapters and I will try not to make so many in future chapters also if you have ideas for how you would like this story to go I would love to hear it I have a basic idea how I want this story to go but I am open to your ideas.**

A week has pasted since Mikey's capture and Raph was starting to get frustrated with all the waiting around; Splinter, Don and April were working out a plan he tried to help out with the plan and he knew he would be leading his family into the Foot's base but he was scared he would mess up again and get someone else hurt or worse… he sighed how does Leo do this all the time how did he make this plans and manage to pull them off. Even with all of Raph's bickering.

Now that Leo was gone he was realizing how much he needed Leo, his only older brother the one everyone went to when they had a problem. Raph wasn't the one to ask for help when he needed it but Leo always seamed to know when any of his brothers were hurting and Leo never asked for Raph to tell him what was wrong like Slinter did; everyone knew Raph was never good with words. No Leo he was just there he would spar with Raph or go running on the roof tops until he felt better.

He was the first one to help and encourage communication if any of them were troubled, yet Leo was a closed book when it came to his own feelings. If Leo had talked to them maybe he would still be here. On the flip side Raph know it was their fault too; none of them bothered to confront Leo about his behavior. If Leo was still here Mikey wouldn't have been captured and Don wouldn't have been hurt everything would be ok.

But he wasn't here now it was up to Raph to protect his family they couldn't want for Leo to come home and save the day, no they would have to save Mikey by themselves.

 **Later**

"ok does everyone know the plan?"

"yes Raph, geese you are starting to sound like Leo." Casey grumbled as everyone got into position Don shared a look at Raph they had the same thought but decided to push it aside for later; because right now they had more important things to think about. Namely finding and recuing Mikey.

"April how's it looking" Don said into his head set.

" _almost there… ok got it the shredders security system is down."_ April said in the head set. April was sitting in the battle shell watching the scene and covering the guys backs while they are in the building. Chasey Raph and Donnie would go in the Saki's tower find Mikey and get him to the battle shell while Splinter prepared the infirmary for a probably injured Mikey.

Inside they begin searching for their youngest brother. After all the times they have broken into the foot's head courters they knew the layout pretty well so they headed strait for the most likely place Mikey would be.

"don't you think it is a little weird that we haven't in countered any foot soldiers?" Donnie asked as they kept to the shadows as much as possible.

"no Don this is a good thing that means they don't know we are here we can get Mikey and get out without Karai ever even knowing we were here." Raph answered

"yeah but shouldn't there be some guards or something?" Don did not like this, there was something wrong and he knew it, He guess Raph didn't feel it. Leo always took their 'feelings' into account if something felt off to one of them then he would change accordingly even if it was nothing he took it seriously; of course, Leo always took their missions seriously and always had a plan, Raph just jumps in head first and always looking for a fight. It wouldn't surprise him is Raph was hoping they would be discovered or find some foot ninja so he could bust so heads for kidnapping their little brother. Don understood that part Mikey was his only younger brother so he was worried about the safety of his younger brother and angry that the foot would even touch him; but this felt off…

"Donnie you worry to much."

"I don't think you worry enough" don retorted

"what is that supposed to mean?" Raph growled giving his brother a sharp look

"guys I don't think this is the time or place for fighting against each other" Casey whispered

"its not like you to take the high road Casey joes." Don said turning to look and the vigilante

"well first time for everything also look." Casey pointed ahead of the group the two turtles turned and saw what their human friend was pointing at. Four-foot soldiers stood guard in front of huge metal double doors which they knew lead down to where Mikey was likely being held.

"see Donnie, guards are you happy now." Raph sarcastically snapped at the purple clad brother. Donnie didn't say anything as they quickly took them out. Donnie worked the lock on the metal door and pushed it open cringing as the door wasn't 'exactly' silent.

"could you do that any louder?" Casey asked as Don just glared at him. The three of them ran in side looking for anymore guards and their little brother.

"Mikey!" Raph's voice drew Dons attention; sitting against the far wall was his only little brother chained and beaten.

"Mikey?" Don asked as he ran up to the cage he was in Mikey wasn't moving

"is he-" Casey didn't finish the sentence Mikey wasn't dead not when they were so close not when Mikey was right here in front of him Mikey was alive and if he wasn't they would still try everything they could to bring him back to life. Don picked the lock on the cage as soon as the bared door opened Raph ran in to see if Mikey was alive. Raph reached out to touch the orange turtle only for his hand to pass right though Mikey's shoulder making his whole form flicker

"what?" all of them said at the same time. Donnie walked over to Raph and tried to touch Mikey but his hand also pashed though the turtle.

"a hologram!" Donnie said shocked

"where is Mikey?" Raph asked

"how am I supposed to know?" Donnie snapped back at Raph just then Laughter filled the chamber the three turned to see Karai and an army of foot soldiers filling the dark hall way.

"oh shell." Don said as he grabbed his bo staff

"where is my little brother! What did you do to him!" Raph shouted not giving Karai a chance to speak as he charges in a blind fury.

They were outnumbered and completely surrounded there seamed to be no way out; but still they fought still they pushed forward.

"Raph we need to go now!" Don shouted Raph looked around and he thought he was going to do his hot head thing and want to stay and finish the fight but when Raph's locked with his, Don was shocked to see pain and sadness in his usual hotheaded brother eyes.

"Casey we are leaving!" Raph shouted and kicked Karai to get some distance between them and ran to join his other two companions, together they broke thought the crow and ran to the nearness exit.

"don't let them escape!" Karai shouted after them but they didn't stop not until they were in the battle shell and safely home did they stop.

"my sons what happened where is Michelangelo?"

"sorry sensei but we failed Mikey wasn't there they have him somewhere else and…"

"it is alright my son we will find him and bring him home." Master Splinter reassured his second eldest son.

'Leonardo please come home soon your family needs you' he thought as his heart ached for his two missings sons and the wreaking family.

 **I hope you liked that chapter.**


	4. Chapter 4

Two days have passed since their failed attempt to save Mikey and it was eating the family apart especially Raph. 'what is taking Leo so long to get back?' he thought he found on more than one occasion that he was going to go to Japan to get his brother back but there was one problem with that plan he had no idea where his brother was in Japan or even who he was with… and he couldn't leave his remaining family behind.

"don have you found anything on the where bouts of Mikey?" he asked getting tired of the silence and his thoughts on his older brother.

"nothing…" don sighed "I don't know when the foot became so good at hiding from us and more importantly more powerful. It's like we are fighting an entirely new enemy."

"there are not new they just have new tricks so we just need to find out how they are doing it so we can get our baby brother back." Raph said

"don't you think I know that but it is a lot easier said than done, Raph…" he sighed again "I am doing the best that I can."

"well, you need to do better!" Raph almost shouted,

"if I didn't know any better Raph I would think that you blame me for not getting Mickey back!" Don shot up from his chair in an uncharacteristic show of rage.

"G-guys?"

"well if we got there sooner, he would probably have still been there!" Raph shouted not backing down

"well if you didn't run in head first like you always do, we probably wouldn't have been Chace out by the foot and we could have found a clue as to where they were keeping our little brother!"

"umm guys I don't think-"

"Oh, so it's all my fault!?"

"Oh, look who figured it out all by himself!"

"why you-"

"Enough!" both boys fell silent at the sound of their father's voice. "what is all this yelling about?" he asked after he got his sons attention

"nothing." The both said shooting a glare at each other and going their separate ways

"Don…" April said trying to calm down her friend

"miss O'Neil" I think it is time for you and Mr. Jones to go home." Master Splinter said. April looked like she wanted to argue but one look forms the old rat told her otherwise

"yes, master splinter please call if you need us, we will be back tomorrow." She said as she got up and grabbed Casey before he could fight back. Once they were gone Splinter spoke

"my sons I know we are in trying times but you still need to work together if we are to find Michelangelo."

"work together sensei we don't know where he is and Raph-" Don was cut off by a stern look from his father

"I know you are trying and both of you are under a lot of stress but you are also still brothers and while Leonardo is… away Raphael is in charge and" he turned to his second eldest "you need to trust in your brother that he is doing everything in his power to locate Michelangelo." Raph just scoffed and turned away.

"why did you send him away?" Raph asked his back still turned to the old rat. "if this family is so lost without him why did you banish him?" He asked again in a more forceful tone when Master Splinter didn't Answer

"Leonardo needed to heal-"

"he needed to Heal! Yeah, he did but you sent him away!"

"Raphael!" splinter raced his voice making the two turtles flinch. "Leonardo has a lot to work through to find himself again and for that, he needed to go away for a little while."

"he has been gone for over two months how long is a little while?" Don asked joining into the conversation splinter didn't have time to respond as the lairs alarm system suddenly when hair wire. Done quirky tuned back to his computer to find out what was going on Master Splinter and Raph joining him.

Suddenly the alarms fell silent

"Don, what's going on?"

"are we in any danger?" his family asked

"I don't understand the alarms shouldn't turn off by themselves if something triggers the perimeter alarm it should keep ringing until I turn it off, it not supposed to turn off by itself." Don was typing furiously "unless someone just deactivated our outer alarm system." Just then something every large started banging on the door to their lair

"well whatever it is it's coming tough the front door!" Raph said palming his sai flowed by Don and his staff and master splinter with is walking stick. They inched closer to the door as the door and some of the surrounding walls were forced in, followed by two red and black robots and an army of foot ninja.

"how did they find us?" Don asked no one in particular

"it doesn't matter how they found us they found us now let's kick the shell out of them!" Raph said swinging his sai but before they jumped into the fight evil laughter filled the lair and Karai enter followed by every emotionless mickey

"Mikey?"

"Michelangelo?" they said in shock at seeing their own with the foot Mikey just smiled

"what did you do to him!?" Raph shouted pointing his one of his sai at the new shredder

"I have done nothing Raphael," she said sweetly "he was just kind enough to give us the location to your lair." Controlled by rage Raph jumped into the sea of foot ninja followed by Don.

"you are controlling him!" Splinter said in barely concealed anger. Karai just chuckled as she attacked the old rat with the help of his youngest son.

"give. Back. My. Brother!" Raph said each world as he fought his way to Karai "and get out of my house!"

"there are too many of them we have to pull back!" Don shouted

"pull back? No way this is our home and they got Mikey I'm not leaving!" Raph shouted to his purple-clad brother as he barely blocked a kick.

 **With master Splinter and Karai**

"so, the daughter of Oroku Saki has become the shredder… why?" Splinter said as Karai began to advance on the old rat.

"honor demands it." She sneered "after you helped the vile Utrom exile my father I vow to avenge his honor!" he dodged a swiped of her clawed glove and dove behind a pillar putting some distance between them.

"You dare speak of honor your father murdered my master and thousands of other begins your father had no honor." Master Splinter said glaring at the new shredder from behind the pillar.

"you will pay for your lies!" she shouted and attacked drawing Splinter out from his hiding spot. "all of you will pay!" she managed to hit him sending him flying into his room where she quickly flowed. "your sons destroyed my father and I will repay them in kind, they will all suffer."

"just like what you have done to Michelangelo?' he asked

"even more so! I begged Leonardo to let him go but he would not listen to reason." She screamed as she crushed the blue orb at her feet and waved the gantlet in the air

"it is you that has been blinded to reason Oroku Saki was a monster a murder, you do not allow yourself to see the truth." The rat said as they circled each other

"I see clearly rat and you will pay for what you have done!" the red eyes of the helmet glaring at the old rat she attacked pushing Splinter back out into the main part of their lair.

"I reached out to you, I hoped you would turn away from evil but now I can see it has consumed you…" he dodged another attack and jumped back but he didn't get far enough away as she sliced him a crossed the chest, "you are faster than your father I will give you that." He grimiest as sticky blood soaked his fur and robe. "but your dark heart will betray you just like it did your father." She attacked again the wound on his chest slowing him down.

"you are not worthy to speak of my father I will silence your traitorous tongue once and for all!"

As the fight continued the turtles were greatly out unnumbered and outmatched and their home was falling apart around them.

"Raph!" Don screamed as he was swallowed by the sea of ninja

"Donnie!" Raph answered searching for his brother when he was attacked from behind stumbling a little, he recovers quickly coming face to face with his little brother.

"Mikey snap out of it!" Raph shouted but his pleas fell on deaf ears as Mikey charged and the fight continues.

Raph thought it would be an easy fight since he knew his brothers fighting style and he had beaten his younger brother countless times but this turtle was not his brother he was different darker and a lot stronger. He was having a hard time fighting back he thought he wasn't fighting at his best because he didn't want to hurt his baby brother but something somewhere deep down, he knew that wasn't true.

"Mikey come on bro this isn't you!" he tried again as Mikey pushed Raph down to the ground, out of the corner of his eye he saw Karai kick master splinter to the floor and he looked really hurt because he was having trouble getting back up. Raph tried to search the lair for his other brother and cursed when he couldn't find him or hear him, he pushed Mikey off he ran to his sensei kicking the surprised krai out of the way before she could deliver the killing blow. Picking up his sensei he ran to the elevator followed by cluck.

"don't let them escape capture the turtle kill the rat!" she shouted as the doors closed.

In the garage Raph stumbled out of the elevator with Master Splinter in his arms, he knocked out six-foot ninja that had followed him in the elevator and he was out of breath. He carried Splinter to the battle shell and started opening the garage door and was surprised to see a bunch of foot ninja waiting for him.

"you have got to be kidding me." He Growled he floored the battle shell with the intention of running them down. But that was still not the end of them as a helicopter appeared hot on his tail. Raph cursed as he waved down the empty streets dodging missiles the best he could. But one hit the back cursing the battle shell to flip and roll down the street. Acting quickly, he unblocked and grabbed Master Splinter and Clunk he got on to the shell cycle and drove it out the back just as another missile hit the van. He raced in the opposite direction from where he came. the helicopter turned to follow but soon lost them in in the allies and other places a helicopter wouldn't fit.

 **Back with Karai**

"tare the filthy place apart leave nothing standing." After she gave the ordered two of the robots started firing at anything in sight targeting the pillars and the walls one even shot a missile to the ceiling. While this was happing, she stood and watched as the home of her enemy fell around her and she laughed at the destruction.

"mistress Karai the one known a Raphael escaped with the rat." One of her minions said thought the com her laughing stopped abruptly

"did we get Donatello?" she asked turning her back in the destruction of the turtle's lair

"yes, Mistress. Michelangelo and some men took him back to headquarters." A different voice said over the com

"excellent."

"Mistress what would you like us to do about the rat and the turtle?" the first voice said

"he will come to me to try and save his brothers we will wait for him. Just prepare Donatello for our control. I will be there soon." She said. She turned back to the entrance of the lair where the two robots were finishing up their destruction of her enemy's home.

"one of you will stay here for the event of Leonardo's return." One of the robots walked to further into the lair singling he would be the one to stay the other one followed Karai back to foot HQ.

 **Well, I hope you liked that chapter. Sorry for the long wait I will try to better at updating more regularly.**


	5. Chapter 5

Raph and splitter that was it both Mikey and Don are gone and Raph barely escaped himself with an injured splinter his home is destroyed and Mikey… poor little Mikey was controlled by the enemy soon don probably be in the same boat. His family was disappearing before his very eyes. Everyone was gone and Splinter wasn't looking too good and without Donnie, he wasn't sure if he was going to survive. 'Leo where are you, bro?' Raph thought to look up at the night sky.

Leo… if he ever did come back there probably won't have a family left to return to. How did it come to this? How did his world fall apart so quickly? A groaned brought Raph out of his thoughts he turned to see Master splinter trying to get up.

"Sensei? You need to rest." Raph said trying to get his father to lay back down.

"wh- where is Donatello?" he said through gritted teeth

"Karai… Karai has him." Raph looked down in shame "I am sorry I failed you…" he said fighting the tears in his eyes

"it is alright my son you did your best…"

"my best? Mikey and Don are gone our home is destroyed and you think that it is ok?" Raph almost screamed he didn't understand what was happing or why his father wasn't yelling at him or giving him disapproving looks like he gives Leo if he did something wrong; so why was he ok with this? " I-I don't understand why are you not angry that I didn't protect this family better since Leo is gone?"

"how could you have known this was going to happen?" Splinter asked his son with pain filled eyes

"Leo would have seen it…" he said Leo would have stopped this before… before this.

"perhaps-" he sighed "Leonardo was trained to strategize you were not so I don't expect you to know everything."

"no, I just run in head first and protect myself… I -I mess everything up Don said we had to leave and now-now he is gone."

"you have done more than I expected my son you did well."

"if you consider getting our family blown apart a good job…" Raph said his anger growing

"no… you held this family together since Leonardo left and you stepped out of your comfort zone of self-protection and for that I am proud of you he wheezed

"wh-what do I do now." Raph asked,

"you go and save your brothers."

"how do I do that? I am not like Leo I can't come up with a plan." Master Splinter just smiled

"don't be Leonardo you are Raphael and I know you will figure something out because you are a protector." He said as he closed his eyes.

"Master Splinter? Master Splinter?" Raph gently shook his father's shoulders but the old rat's eyes remained closed Raph began to panic "father? Please don't do this to me I can't lose you to please wake up!" Raph being but Splinter did not open his eyes.

after several minutes rage-filled Raph; Karai did this and she will pay he will get his brothers back. He reaped over and over in his head that he would get his brothers back. He played Splinter back down and wiped the tears from his eyes. It was time to get his family back.

 **Foot HQ**

"how is Donatello doing?" Karai asked one of her scientists as she walked into the foot lab

"Donatello has proven… more difficult to control then Michelangelo." Said the scientist careful not to anger his mistress "but we are using the doses and will be ready to test it in a couple of hours" he said quickly

"excellent" she said stopping in front of an unconscious turtle strapped to a table and a weird looking device hooked up to his head. "and how is Michelangelo?" as if on cue another turtle walked in and bowed when he got to Karai

"he is doing well all test were a secure will no ill effects he will only follow your orders." The scientist said with pride as he watched the turtle get back to his feet. He didn't look like Michelangelo anymore now he had a black mask with his red eyes and all of his gear had been changed to foot equipment.

"have you fixed that one problem?" the New shredder asked as she observed the young turtle.

"yes, he is now able to answer questions and talk when you wish it."

"good." She nodded "Michelangelo tell me who do you serve?" she asked and without missing a beat Michelangelo answered

"I serve you and the foot clan." He said with no emotion

"how else do you serve?"

"no one." He said again without hesitation. Karai smiled

"tell me where is Leonardo?"

"I do not know." Karai's smile faltered as she turned to look at the scientist with a glare

"do you know when he will return?" she tried again turning back to face the turtle

"no." came the short reply

"Mistress everything is working to your specifications so he is not lying he can't lie to you that means he really doesn't know." The scientist says as he checked his pad with a shaking hand

"very well I will try with the other one as soon as he is ready." She said turning to walk away.

 **Later that night**

Raph was silently running across rooftops until he had the foot HQ insight, he stopped to catch his breath.

'Karai will pay for this.' He thought and quickly jumped to the flat part of the foot building knocking out the guard on duty and ran inside looking for his brothers he needed to get them out first then come back for Karai.

He fought and fought but that was not enough he too fell at the hands of Karai and his brothers he Wasn't enough to save them he tried and failed and now the Hamoto family was gone and the worst part of this Leo would come home and he would have lost his family he would probably blame himself for not being there but in truth it was all Raph's fault for trying to be like Leo for not listening for failing. That was his last thought as he drifted off into the darkness foot robots dragging him to his fate.

All that remains is Leonardo

Karai walked into April's shop in a black trench coat and hat and briskly walked to the back of her store pick up a vase and pretending to examine the artwork on the side.

"I will be with you in just a moment…" April said as she continued to help the only other person in the story. Karai could see the pain and worry in April's eyes as she pretending like nothing was bothering her. At the thought of her pain, the head of the foot clan smiled.

"thank you for waiting how may I help you?" she said with false enthusiasm.

"I am looking for Leonardo," Karai said her back still facing April

"Leo?... I don't know anyone by that name." she lied

"let us not play games Miss O'Neill, have you seen him of late?"

"how do you know Leo? Who are you?" April said growing more nervous

"I was hoping to leave him a message." She said slowing walking to the counter

"ookay… what is it?"

"let him know that I have his family and if he what's to see them again he will surrender himself to me." Karai said finally lifting her head and dropped the turtle's sign that said "sewer sweet sewer." April gasped at the sign then looked up to see who had dropped it and she gasped again and took a step back.

"Ka-Karia?!" Karai didn't say anything just smiled as she turned to walk out into the busy New York streets.

'soon Leonardo you will be mine, I will taste your blood and truly revenge my father.' She thought as she disappeared

 **Hi everyone I would like to let you know this story won third place for best villain** **so thanks everyone and I am glad you our enjoying this story**


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